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Old 12-06-2011, 03:45 PM   #1
simon.jarman@aad.gov.au
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Default ion torrent barcode sequences

I am trying to discover the sequences of the barcodes used in the ion Torrent barcoding kit. The Torrent Server doesn't sort files by barcodes unless you are doing genome sequencing for some weird reason, so for sequencing environmental amplicons I will have to do this with a script. However, the barcodes on the Torrent Server software are 11 bp long, the barcode kit manual says the barcodes are 10 bp long and nobody at Life Tech seems to be able to provide any information on this, in keeping with their apparent policy on keeping everything about this system as secret as possible. If anyone has more knowledge than me on this, I'd be grateful for them to share it.

PS: Anyone want to buy a slightly used Ion Torrent?
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Old 12-06-2011, 05:41 PM   #2
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Hi Simon,

I believe your questions have already been answered and I've also sent you a PM. None of what you've asked for is secret information. My sincere apologies if you've encountered any delays in getting the information you needed.
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Old 12-06-2011, 08:21 PM   #3
genseq
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Price for Russia:
4471250 Ion XpressTM Barcode Adaptors 1‐16 Kit (160 реакций) - 3 272$
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Old 12-06-2011, 08:32 PM   #4
simon.jarman@aad.gov.au
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Very competitive pricing...
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Old 12-06-2011, 11:32 PM   #5
genseq
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Quote:
Originally Posted by simon.jarman@aad.gov.au View Post
PS: Anyone want to buy a slightly used Ion Torrent?
How much does it cost?
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Old 12-12-2011, 10:30 PM   #6
singaporeseq
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Why are you selling?
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Old 12-14-2011, 06:05 PM   #7
kenietz
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Hi,
how can one manually separate the reads by barcodes coming from the PGM? We got FASTQ and SFF but the reads are not separated by barcodes. Is there a tool or script or something?

Thank you
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Old 12-14-2011, 06:27 PM   #8
simon.jarman@aad.gov.au
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There is a bug in the Torrent Server software as of the current 1.5 version that means that it won't sort barcodes for you unless you specify a reference sequence to compare against, even if you don't have one for your amplicons / fragments. If you have done a run with barcoded adapters/fusion primers then you can re-analyse it on the Torrent Server making sure you tick the 'reference' sequence for the E.coli control sequence. It will then give you separate FASTQ files for each barcode.

Another option is just to use a script to do it yourself. This lab has produced a good bunch of scripts for this and other sequencing processing tasks:

http://hannonlab.cshl.edu/fastx_toolkit/
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Old 12-14-2011, 06:39 PM   #9
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Hi Simon,
thank you very much for the fast and informative answer. I will check the scripts for sure and will tell the lab guys to do as you suggested for next runs.

Cheers
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Old 03-05-2012, 10:28 AM   #10
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Default designing Ion Torrent barcode sequences

Are there any rules how to design new barcodes for Ion Torrent? We have used successfully our 454 amplicon primers, but now we have to add more primers. I am not sure, but the barcode sequence is optimized for the order of nucleotide flow? Is this known for Ion Torrent and are there any public lists of IT barcodes (for 454 there are many)?
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Old 05-02-2012, 02:06 AM   #11
Fisher.R
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Default ion seq

Quote:
Originally Posted by IonTorrent View Post
Hi Simon,

I believe your questions have already been answered and I've also sent you a PM. None of what you've asked for is secret information. My sincere apologies if you've encountered any delays in getting the information you needed.
Hi there Ion man.
I planning an IT experiment with HIV seq but I'm also struggling to find the barcode sequences. Could please send me a link or maybe the sequences?

Best regards.
RF.
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Old 06-02-2012, 02:17 AM   #12
genseq
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Cool

Look here:
Attached Files
File Type: pdf Barcoding.pdf (315.0 KB, 1158 views)

Last edited by genseq; 06-03-2012 at 09:03 PM.
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Old 06-06-2012, 08:29 AM   #13
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Quote:
Originally Posted by Fisher.R View Post
Hi there Ion man.
I planning an IT experiment with HIV seq but I'm also struggling to find the barcode sequences. Could please send me a link or maybe the sequences?

Best regards.
RF.
Hi RF,

you can find the full set of 96 barcodes (adaptors with barcodes 1 - 16 and 17 - 32 are available as commercial kits if that option is of interest) at this location on the Ion Community:
http://lifetech-it.hosted.jivesoftwa.../docs/DOC-2346
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Old 06-06-2012, 01:18 PM   #14
IonTorrent
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I should also mention that as announced today, the full set of 96 barcoded adapters is now available as a kit (Ion Xpress™ Barcode Adapters 1-96 Kit):

http://products.invitrogen.com/ivgn/product/4474517
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Old 07-28-2012, 12:34 AM   #15
genseq
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Cool Barcoding for all

English version:
Attached Files
File Type: pdf seq4all_Barcoding.pdf (315.7 KB, 1191 views)
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Old 08-03-2013, 12:32 PM   #16
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Greetings all,

Thanks for the info!

If e.g. the barcode 1 oligos are aquired then, how should these be prepared and at what concentrations?
Should the long and short sequences just be diluted to an appropriate stock concentration and then simply mixed together or should they be pairwise annealed somehow prior to ligation (or perhaps just ordered as a duplex)?

Throughout all available manuals and guides only adapter volumes seem to be mentioned, but I haven't been able to find a single place where the actual concentration of the adapter solutions are mentioned in any of these manuals. Does anybody know what concentrations should be used? (I.e. what are the stock concentrations in the Ion Xpress barcode adapter kits)

Also, I do not understand why the overlap between the barcode adapters are not similar to the overlap between the non-barcoded adapters, i.e. in the non-barcoded adapters there is a T*T* overhang from the complementary sequence while there is a 13-base non-overlapped sequence in all the barcoded adapters. Why might this be so?

Best regards
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